Tag: epigenetics

There are no mechanisms for macroevolution

Epigenetic markers strongly affect binding of transcription factors

Epigenetic Marks Shun Some Transcription Factors, Embrace Others

Excerpt: “The same epigenetic marks can be read as “keep off” or “welcome,” depending on what DNA-binding protein, or transcription factor, is doing the reading. These marks, methylated cytosine and guanine dinucleotides (mCpGs), normally indicate which portions of the genome are inactive. But new findings from a systematic study of hundreds of transcription factors suggest that mCpGs may play a more subtle role in gene regulation.

In this new study, scientists based at Karolinska Institutet systematically analyzed the binding specificities of transcription factors to DNA that was marked by mCpGs, as well as to DNA that was unmarked by mCpGs. The observed that mCpGs can influence binding of most transcription factors to DNA—in some cases negatively and in others positively.

Interestingly, many of the transcription factors that prefer to bind to mCpG sites appear to be important to development. This finding may inform future analyses of the role of DNA methylation on cell differentiation, chromatin reprogramming, and transcriptional regulation.

The results pave the way for cracking the genetic code that controls the expression of genes, and will have broad implications for the understanding of development and disease. The availability of genomic information relevant to disease is expanding at an exponentially increasing rate.

“This study identifies how the modification of the DNA structure affects the binding of transcription factors, and this increases our understanding of how genes are regulated in cells and further aids us in deciphering the grammar written into DNA,” noted Professor Taipale.””

Excerpt from the original study:

“One shortcoming is the lack of knowledge about DNA binding specificities (motifs) for hundreds of the estimated ~1600 human transcription factors. Another is how transcription factor binding is modulated by “epigenetics”—a contentious term that refers to heritable states of both cells and organisms, as well as the covalent chemical modifications of DNA and protein that often provide the underlying mechanism. DNA methylation at cytosine and guanine dinucleotides (mCG) satisfies most views of epigenetics, as it is inherited across cell divisions and functions in imprinting (parent-of-origin–dependent gene expression). On page 502 of this issue, Yin et al. provide a comprehensive look at the extent to which human transcription factor binding is affected by mCG, and make a striking finding: Many homeodomain transcription factors—perhaps the best characterized developmental regulators in biology can bind to specific methylated DNA sequences.

More generally, the study of Yin et al. contributes a unique perspective to evaluating how transcription factors bind DNA. Transcription factor motif modeling is critical for the study of global gene regulation, allowing us to predict potential binding sites in the genome. Given that so many transcription factors are affected by chemical modifications to DNA, we are now faced with a clear necessity to incorporate DNA methylation into motif models, and a new type of data from which to learn to read the genome the way transcription factors do.”

My comment: This study confirms my previous claims about factors affecting phenotypes of organisms and observed changes in nature. Alterations in organisms are based on epigenetic factors and designed mechanisms mediated by nutrition, stress, climate and other environmental factors. Even one addition or deletion of one methyl group on a gene might have a significant influence on cell activity and identity. Random mutations or natural selection have no role in biodiversity. There are no mechanisms for large scale evolution. Everything points to God’s design and creation.

Genetically identical twins – but not so identical traits

Genetically identical twins – but not so identical traits

Identical twins with different skin, hair and eye colors – Gene sequences don’t determine traits

Excerpt: “Two baby girls from County Durham are thought to be the first genetically identical twins in the UK to be born with different eye and skin colour.

Before their birth, placental sampling had shown the twins were monozygotic – they had developed from the same fertilised egg and share the same DNA sequence.
‘Alternatively, sometimes markers on the DNA which influence the extent to which the DNA is expressed can be different in the twins. We do have some evidence that skin colour is subject to this kind of “epigenetic'” control,’ Dr Steves added.”

https://www.sciencedaily.com/releases/2017/04/170419121955.htm#.WPiYgwpqTIg.linkedin
(April 19, 2017)

Excerpt: “Although identical twins have the same genes as each other, their epigenomes — the collection of methyl marks studding their DNA — are different by the time they reach adulthood due in part to environmental factors. Reprogramming the skin cells of adult identical twins to their embryonic state eliminated most of these differences, the researchers found when they studied cells from three sets of twins. However, there were still key epigenetic differences between twins in terms of how the iPSCs compared to ESCs.

“In the past, researchers had found lots of sites with variations in methylation status, but it was hard to figure out which of those sites had variation due to genetics,” says Panopoulos. “Here, we could focus more specifically on the sites we know have nothing to do with genetics.” That new focus, she says, is what allowed them to home in on the MYC binding sites.”

My comment: Human skin, hair or eye colors are not determined by gene sequences. Instead, traits are determined by epigenetic control of gene expression. Some of the epigenetic markers can be very stable. Histone methylation marks can be passed on for at least 14 generations according to a new study:

https://www.sciencedaily.com/releases/2017/04/170420141753.htm#.WPnaAiBOiGs.twitter

These findings destroy pseudoscientific claims about mutations made by population genetics. There is no such a thing as a human race. We are all the same, human beings, created by God.

Scientists should place these facts in the context of ecological adaptation and variation within kinds. There are no mechanisms for large scale evolution. Don’t get lost.

The existing species concept called into question

The existing species concept called into question

Bears breed across species borders – ‘Species’ is a man made word

https://www.sciencedaily.com/releases/2017/04/170419093151.htm#.WPikcs4L-8M.linkedin

Excerpt: “Pizzly, grolars or “capuccino bears” are common names of the offspring resulting from the mating of grizzly bears (Ursus arctos) and polar bears (Ursus maritimus). “Such hybrids among bears are not as rare as we have hitherto assumed,” says Prof. Dr. Axel Janke of the Senckenberg Biodiversity and Climate Research Center in Frankfurt. In a large-scale analysis, a team of scientists led by the German evolutionary geneticist has sequenced six complete bear genomes. Each genome is about 2.5 billion base pairs large. “With these new data of the sun bear, sloth bear, Asiatic black bear and spectacled bear, we now have the genomes of all known bear species,” adds Janke.

It has previously been assumed that the number of hybrids between polar and brown bears is increasing due to climate change, because brown bears invade northern regions and polar bears move onto the sea ice later than usual. The new results show however that an abundant flow of genes among different bear species occurred to a good deal in the past. Hybrids are thus not necessarily linked to climate change. “Bears can form hybrids in different combinations,” explains Janke, and adds: “We knew this from zoos. In the wild, so far this was only observed for polar bears and brown bear as well as Asiatic black and sun bear.”

The new genomic data also show that there must have even been gene flow between the polar and sun bears. However, the two species live in geographically completely distinct areas and thus have never met.

The detected gene flow among bears also questions the basic biological concept of a species. The biological species definition assumes that different species cannot produce offspring in the wild or that hybrid offspring are sterile. The best-known example of this is the mule — a hybrid between a horse and a donkey. However, it has been observed that grolars, the hybrids between polar and grizzly bears, are often fertile. Janke: “We have to ask ourselves: Does the species concept still hold true, given there is evidence of gene flow not only in bears, but also in other animals?”

My comment: Why are they surprised after observing Bear variation which is based on epigenetic control of gene expression? Bears are just adapted to different environments, different diet and climate and that’s why they look a bit different. But actually they are the same kind. That’s why they are able to breed and get fertile offspring.

‘Species’ is a pseudoscientific term used for maintaining evolutionary illusions. Adaptation to different diets and climate leads to loss of biological information due to genetic mutations. An intensive loss of information might cause even chromosome loss and this can affect the mating willingness and even cause chromosomal barriers for breeding. Different looking bears are not willing to mate in the wild due to control of pheromones but in captivity we can observe interesting cases of hybridization. For example, the Red Muntjac has the lowest diploid chromosomal number in mammals (2n = 6 for females and 7 for males) whereas Reeves’ Muntjac has 2n = 46. But still these two species can produce viable F1 hybrids in captivity.

Everything points to Biblical creation and rapid variation of kinds. Don’t get misled.

Seven things Darwin didn’t tell you

Seven things Darwin didn’t tell you, because he didn’t know.

1. Alterations in diet, climate, stress and other environmental factors cause mechanism based inheritable changes in organisms, not random mutations and selection.

An example: Italian wall lizards experienced radical changes in morphology and behavior after changing their diet from insects to plants. This occurred very rapidly, just in three decades. They even had a ‘new’ structure in their gut, so called Cecal Valve. Genes that control growth of the Cecal Valve were differently expressed due to the changed diet.

2. Random mutations don’t enhance the genomic information. Random mutations are genetic errors and they destroy biological information and disrupt genetic integrity.

An example: There are about 200,000 disease-causing genetic mutations in the human DNA pointing out that evolution is not happening and that so called natural selection is not able to weed those mutations out.
3. Most of so-called mutations are not random changes. Genetic changes occur due to oxidative stress, changing diet, exposure to toxins, disrupted methylation patterns, viruses etc. However, most of them still disrupt genetic integrity.
Examples:
– A lack of methyl groups in gene body may develop cancer and trigger genetic mutations.
– Viruses play a potential role in causing aberrant methylation patterns. According to a fresh study, more than 1 in 5 adults has cancer-causing HPV infection.
4. Biological information is multi-layered. There are at least three forms of biological information in the cell:
1. Gene sequences – Digital information layer
2. Epigenetic markers, 3D genome, flanking binding sites – Analog information layer
3. Gene regulatory networks, genomic integrity and stability – Meta data
Examples:
– The cell uses cytokines as knobs instead of switches.
– DNA methylation influences continuous variation in ant worker size
5. Biological information is extremely complex. The ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world.
6. Organisms can experience rapid variation due to epigenetic mechanisms.
7. Life is not driven by gene sequences. Genes are driven by lifestyle.
That’s why Intelligent Design and Creation. Don’t get lost.

How millions of years changed to thousands

How to make a cave fish in just a few thousand years

Excerpt: “How long does it take for a cave fish to evolve from an open-water swimmer? Only a few thousand years, according to a new study. Scientists used to think that ice age glaciers covering northern Europe had prevented fish from colonizing the continents’ caves. Such species were thought to live no farther north than Pennsylvania’s Nippenose Valley. But a new cave-dwelling fish discovered in southern Germany 2 years ago is turning that assumption on its head. The pale, tiny fish with long, whiskerlike barbs sprouting from its head (above) is a new species of loach, as yet unnamed. It’s also the first cave fish to be found in Europe, 760 kilometers farther north than those in Pennsylvania.

Until 12,000 years ago, Europe and its caves were buried beneath glacial ice, which blocked any connection between above- and underground waterways. But as the glaciers retreated, sinkholes and springs formed around Germany’s upper Danube, connecting the river to extensive caves and streams 250 kilometers below. Some fish made their way in, becoming smaller, with pale scaleless bodies, large nostrils, and tiny eyes—all adaptations for living in the dark, the scientists report in today’s issue of Current Biology. Based on their genetic analysis, the scientists say the cave loach is a close relative of the darkly mottled stone loach, which is twice the size of the cave fish, and still swims in the sunny, open waters of the Danube River.”

My comment: Previous pseudoscientific studies claimed that the blind cave fish gradually experienced mutations during millions of years and that natural selection helped the fish to evolve and adapt to dark, lightless environment. Incredible nonsense! How many ‘scientific’ studies were made using this claim as a starting point? And people believed in them! Of course, because science, the god of wisdom, so claimed. How sad.

Modern scientists already understand that adaptation for living in the dark doesn’t take even thousands of years. Instead, it can happen just in tens of generations. And not a single gene sequence alteration is needed for this clever adaptation procedure. How is it done?

There are opsins, light-sensitive proteins in fish skin, eyes and brain. Information of light level is transmitted into neurons in the brain and based on this, certain genes are regulated by epigenetic mechanisms. The necessary information for embryonic gene regulation is transmitted by microRNAs. By this clever, designed mechanism, the blind cave fish is able to rapidly activate it’s eyes after returning into normal environment. It takes only a few generations.

Random mutations or natural selection has no role within these designed mechanisms. Everything points to God’s creation and Intelligent Design. Don’t get lost.